library(tidyr)
library(dplyr)
## 
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
## 
##     filter, lag
## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union
library(ggplot2)
library(plotly)
## 
## Attaching package: 'plotly'
## The following object is masked from 'package:ggplot2':
## 
##     last_plot
## The following object is masked from 'package:stats':
## 
##     filter
## The following object is masked from 'package:graphics':
## 
##     layout
library(manhattanly)
## See example usage at http://sahirbhatnagar.com/manhattanly/
assoc_logistic <- read.table(file="/Users/vicegill/Documents/gemma_output.assoc.txt",header=TRUE)
assoc_logistic_filter <- assoc_logistic %>%
                      dplyr::filter(assoc_logistic$p_wald < 0.005)
assoc_logistic_filter$chr =as.numeric(assoc_logistic_filter$chr)
assoc_logistic_filter <- assoc_logistic_filter %>% filter(!is.na(chr))
manhattan_obj <- manhattanr(assoc_logistic_filter,chr="chr",bp="ps",p="p_wald")
manhattanly(manhattan_obj)